cosmic-database

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# COSMIC Database

## Overview

COSMIC (Catalogue of Somatic Mutations in Cancer) is the world's largest and most comprehensive database for exploring somatic mutations in human cancer. Access COSMIC's extensive collection of cancer genomics data, including millions of mutations across thousands of cancer types, curated gene lists, mutational signatures, and clinical annotations programmatically.

## When to Use This Skill

This skill should be used when:
- Downloading cancer mutation data from COSMIC
- Accessing the Cancer Gene Census for curated cancer gene lists
- Retrieving mutational signature profiles
- Querying structural variants, copy number alterations, or gene fusions
- Analyzing drug resistance mutations
- Working with cancer cell line genomics data
- Integrating cancer mutation data into bioinformatics pipelines
- Researching specific genes or mutations in cancer contexts

## Prerequisites

### Account Registration
COSMIC requires authentication for data downloads:
- **Academic users**: Free access with registration at https://cancer.sanger.ac.uk/cosmic/register
- **Commercial users**: License required (contact QIAGEN)

### Python Requirements
```bash
uv pip install requests pandas
```

## Quick Start

### 1. Basic File Download

Use the `scripts/download_cosmic.py` script to download COSMIC data files:

```python
from scripts.download_cosmic import download_cosmic_file

# Download mutation data
download_cosmic_file(
    email="your_email@institution.edu",
    password="your_password",
    filepath="GRCh38/cosmic/latest/CosmicMutantExport.tsv.gz",
    output_filename="cosmic_mutations.tsv.gz"
)
```

### 2. Command-Line Usage

```bash
# Download using shorthand data type
python scripts/download_cosmic.py user@email.com --data-type mutations

# Download specific file
python scripts/download_cosmic.py user@email.com \
    --filepath GRCh38/cosmic/latest/cancer_gene_census.csv

# Download for specific genome assembly
python scripts/download_cosmic.py user@email.com \
    --data-type gene_census --assembly GRCh37 -o cancer_genes.csv
```

### 3. Working with Downloaded Data

```python
import pandas as pd

# Read mutation data
mutations = pd.read_csv('cosmic_mutations.tsv.gz', sep='\t', compression='gzip')

# Read Cancer Gene Census
gene_census = pd.read_csv('cancer_gene_census.csv')

# Read VCF format
import pysam
vcf = pysam.VariantFile('CosmicCodingMuts.vcf.gz')
```

## Available Data Types

### Core Mutations
Download comprehensive mutation data including point mutations, indels, and genomic annotations.

**Common data types**:
- `mutations` - Complete coding mutations (TSV format)
- `mutations_vcf` - Coding mutations in VCF format
- `sample_info` - Sample metadata and tumor information

```python
# Download all coding mutations
download_cosmic_file(
    email="user@email.com",
    password="password",
    filepath="GRCh38/cosmic/latest/CosmicMutantExport.tsv.gz"
)
```

### Cancer Gene Census
Access the expert-curated list of ~700+ cancer genes with substantial evidence of cancer involvement.

```python
# Download Cancer Gene Census
download_cosmic_file(
    email="user@email.com",
    password="password",
    filepath="GRCh38/cosmic/latest/cancer_gene_census.csv"
)
```

**Use cases**:
- Identifying known cancer genes
- Filtering variants by cancer relevance
- Understanding gene roles (oncogene vs tumor suppressor)
- Target gene selection for research

### Mutational Signatures
Download signature profiles for mutational signature analysis.

From Zaoqu-Liu/ScienceClaw, MIT.

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